Each have their positives. If you are an elite player who is viewed as a likely first rounder, the CHL is probably the best route. The positives of the CHL include this (in purely hockey terms). More games, fewer restrictions on practice times, and no grade obligations, it also tends to offer higher level competition from 16-18 than the traditions NCAA paths. NCAA has benefits. You get to choose your team, I feel this is a big positive for the NCAA. While CHL guys can somewhat force there way to teams or out of bad developmental systems, in the NCAA you outright choose who you want to play for. Secondly, it tends to offer better facilities for physical off-ice training. Finally, it gives you more time to prove you are pro-ready for late-bloomers.
So, I'd say this, if you are viewed as a legitimate top 60 pick, I'd probably go CHL, but past that, NCAA is the way to go. I'd also lean NCAA for almost all goaltenders. D is a mixed bag but possibly an NCAA lean, highly skilled forwards I would lean CHL.
The other issue you get into is not all CHL leagues are equal in developmental quality or lifestyle. The WHL is a hell of a grind for a 16 year old, and the QMJHL has lowered in quality over the years. While not all NCAA conferences are equal, as pointed out earlier, as a top talent you choose what program and division you go to.